How can I make duplicates of an object using empties as placeholders?
First select the cube and create a group Ctrl + G

Then select all your empties and go to the Properties Panel > Object > Duplication click Group and then choose the newly created group from the dropdown.



If you have selected more than one empty, hit Ctrl + L with all of them selected and click on DupliGroup to have the Group property copied to all of them.